Many devices use an ion source or an electron source to provide ions or particles. During use of the ion source it may become contaminated with sample or due to exposure to the atmosphere, or other unwanted species can accumulate on the source components potentially resulting in poor performance or analysis errors. It may be desirable to remove the source for cleaning, but removal of the source can lead to contamination of the instrument when the source is not in place, for example, due to exposure to atmosphere. In particular, the entire instrument may need to be opened to remove and clean the ion source, which can lead to contamination of internal components of the system. In addition, proper column positioning in an instrument can affect overall instrument performance.